I got the solution for my own question :)
In df command you can pass the file system types which you would like to
exclude, in this case it is 'fuse.gvfs-fuse-daemon'.
So when I execute the below the command I no more get this message "df:
`/root/.gvfs': Permission denied"
df -x fuse.gvfs-fuse-daemon
For more details one can look into df --help option.